Papers by Penelope Rodriguez-Zamora
Computational and Theoretical Chemistry
Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magn... more Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the protein with lower resolution, but revealing domain positions. Different conjugation methodologies use the complementarity of both technique ́s independent constraints to accomplish a comprehensive protein structure determination and dynamics understanding at a moderate computational expense.
Langmuir
Cysteine-protected metal nanoparticles (NPs) have shown interesting physicochemical properties of... more Cysteine-protected metal nanoparticles (NPs) have shown interesting physicochemical properties of potential utility in biomedical applications and in the understanding of protein folding. Herein, cysteine interaction with gold, silver, and copper NPs is characterized by Raman spectroscopy and density functional theory calculations to elucidate the molecular conformation and adsorption sites for each metal. The experimental analysis of Raman spectra upon adsorption with respect to free cysteine indicates that while the C-S bond and carboxyl group are similarly affected by adsorption on the three metal NPs, the amino group is sterically influenced by the electronegativity of each metal, causing a greater modification in the case of gold NPs. A theoretical approach that takes into consideration intermolecular interactions using two cysteine molecules is proposed using a S-metal-S interface motif anchored to the metal surface. These interactions generate the stabilization of an organo-metallic complex that combines gauche (PH) and anti (PC) rotameric conformers of cysteine on the surface of all three metals. Similarities between the calculated Raman spectra and experimental data confirm the thiol and carboxyl as adsorption groups for gold, silver, and copper NPs and suggest the formation of monomeric "staple motifs" that have been found in the protecting monolayer of atomic-precise thiolate-capped metal nanoclusters.
Small, 2021
Gold, silver, and copper small nanoparticles (NPs), with average size ≈2 nm, are synthesized and ... more Gold, silver, and copper small nanoparticles (NPs), with average size ≈2 nm, are synthesized and afterward protected with l- and d-cysteine, demonstrating emergence of chiroptical activity in the wavelength range of 250-400 nm for all three metals with respect to the bare nanoparticles and ligands alone. Silver-cysteine (Ag-Cys) NPs display the higher anisotropy factor, whereas gold-cysteine (Au-Cys) NPs show optical and chiroptical signatures slightly more displaced to the visible range. A larger number of circular dichroism (CD) bands with smaller intensity, as compared to gold and silver, is observed for the first time for copper-cysteine (Cu-Cys) NPs. The manifestation of optical and chiroptical responses upon cysteine adsorption and the differences between the spectra corresponding to each metal are mainly dictated by the metal-ligand interface, as supported by a comparison with calculations of the oscillatory and rotatory strengths based on time-dependent density functional theory, using a metal-ligand interface motif model, which closely resembles the experimental absorption and CD spectra. These results are useful to demonstrate the relevance of the interface between chiral ligands and the metal surfaces of Au, Ag, and Cu NPs, and provide evidence and further insights into the origin of the transfer mechanisms and induction of extrinsic chirality.
Advances in Biological Chemistry, 2020
Glycine crystallizes into three different polymorphs called α, β and γ under standard physicochem... more Glycine crystallizes into three different polymorphs called α, β and γ under standard physicochemical conditions. They have different features depending on their structural variations. The possible interaction of glycine with magnetic minerals in meteorites and comets or in the ancient Earth, paves the way to study the self-assembly and molecular behavior under irradiation and magnetic conditions. The magnetic field might induce the formation of a specific polymorph of glycine. To gain insight on the consequences of gamma irradiation with a gradient of static magnetic fields (0.06 T, 0.3 T, 0.42 T and 0.6 T) on the self-assembly of single macroscopic glycine crystals, we gamma irradiated the powdered amino acid and then assembled single crystals from water solutions. The preliminary results showed a stable formation of fluid inclusions in the single crystals and no straightforward effect on the self-assembly process after glycine gamma irradiation and interaction with static magnetic fields. The α glycine polymorph single crystals formed at 55˚ from the magnetic longitudinal axis and seemed to be enhanced by gamma radiation.
Communications Biology, 2020
Plakin proteins form connections that link the cell membrane to the intermediate filament cytoske... more Plakin proteins form connections that link the cell membrane to the intermediate filament cytoskeleton. Their interactions are mediated by a highly conserved linker domain through an unresolved mechanism. Here analysis of the human periplakin linker domain structure reveals a bi-lobed module transected by an electropositive groove. Key basic residues within the periplakin groove are vital for co-localization with vimentin in human cells and compromise direct binding which also requires acidic residues D176 and E187 in vimentin. We propose a model whereby basic periplakin linker domain residues recognize acidic vimentin side chains and form a complementary binding groove. The model is shared amongst diverse linker domains and can be used to investigate the effects of pathogenic mutations in the desmoplakin linker associated with arrhythmogenic right ventricular cardiomyopathy. Linker modules either act solely or collaborate with adjacent plakin repeat domains to create strong and ada...
Journal of Raman Spectroscopy, 2019
Understanding the physical mechanisms of thiolated molecules adsorption on metal surfaces has req... more Understanding the physical mechanisms of thiolated molecules adsorption on metal surfaces has required copious research, particularly on Au-cysteine systems due to the affinity of sulfur molecules to gold surfaces, as well as the interesting structural modifications that this strong interaction induces and the peculiar optical, chiroptical, and electronic properties of Au(SR) systems. Here, we present vibrational experimental data on the adsorption of Land D-cysteine on small gold nanoparticles (<2 nm) by means of Raman spectroscopy. Land D-cysteine molecules adopt the same strained conformation upon adsorption on colloidal gold nanoparticles, regaining structure due to the stabilization that the gold nanoparticle induces on the cysteine, reflected in the recuperation of vibrational bands from their polymorphically distinctive crystalline forms. Through the analysis of Raman vibrational modifications after adsorption, we found experimental evidence that confirms a stabilized cysteine conformation locating the carboxyl group in the antiposition (P C isomeric rotamer) for both molecules. This result is supported by extensive density functional theory (DFT) calculations and simulated Raman spectra, considering zwitterionic cysteine adsorbed on a Au 34 cluster, emulating experimental nanoparticle sizes. Our Raman spectroscopy experimental and DFT results determine one of the oxygen atoms of the carboxyl group as a second adsorption site after the sulfur atom, confirming that independent of its polymorphism and enantiomerism, zwitterionic cysteine interacts with gold nanoparticles through the thiol group and the carboxyl group as adsorption sites.
Progress in Biophysics and Molecular Biology, 2019
Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magn... more Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the protein with lower resolution, but revealing domain positions. Different conjugation methodologies use the complementarity of both techniques' independent constraints to achieve comprehensive protein structure determination and resolve dynamics at a moderate computational expense.
Polymer Engineering & Science, 2019
Dextrin and dextrin-polyethylene oxide (DEX/PEO) fibers in the submicron range were produced by e... more Dextrin and dextrin-polyethylene oxide (DEX/PEO) fibers in the submicron range were produced by electrospinning of single and blend polymer solutions. The morphology, intermolecular interactions, and mechanical properties of dextrin microfibers with and without PEO were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray diffraction, nuclear magnetic resonance spectroscopy, and uniaxial tensile testing. Spectroscopic results confirmed hydrogen bond formation, evidencing dextrin as a molecular entanglement source for fiber mechanical reinforcement. The uniaxial tensile tests demonstrated a synergistic mechanical reinforcement effect that varied with blend composition. Equal weight ratio blends supported a maximum tensile strength with a high elastic modulus and demonstrated to be more elastic and resistant to breaking, even than pristine PEO fibers. Moreover, elastic moduli of blend fiber mats were found to lie within the value range for human skin, thus providing the DEX/PEO meshes with potential applicability as skin tissue scaffolds. This synthesis approach proved the feasible and inexpensive fabrication process of natural-synthetic polymer hybrid fibers that combine the biocompatibility, biodegradability, and encapsulating capability of dextrin with the mechanical strength and flexibility of PEO for the development of scaffolds for tissue engineering and topical drug delivery applications in skin wound healing.
Nature communications, Jan 3, 2016
Plakin proteins form critical connections between cell junctions and the cytoskeleton; their disr... more Plakin proteins form critical connections between cell junctions and the cytoskeleton; their disruption within epithelial and cardiac muscle cells cause skin-blistering diseases and cardiomyopathies. Envoplakin has a single plakin repeat domain (PRD) which recognizes intermediate filaments through an unresolved mechanism. Herein we report the crystal structure of envoplakin's complete PRD fold, revealing binding determinants within its electropositive binding groove. Four of its five internal repeats recognize negatively charged patches within vimentin via five basic determinants that are identified by nuclear magnetic resonance spectroscopy. Mutations of the Lys1901 or Arg1914 binding determinants delocalize heterodimeric envoplakin from intracellular vimentin and keratin filaments in cultured cells. Recognition of vimentin is abolished when its residues Asp112 or Asp119 are mutated. The latter slot intermediate filament rods into basic PRD domain grooves through electrosteric ...
Desmoplakin is a cytolinker protein that establishes connections with the cell cytoskeleton and t... more Desmoplakin is a cytolinker protein that establishes connections with the cell cytoskeleton and to anchoring junctions at the cell membrane, providing the adaptable structural rigidity within the skin and heart cells required to accommodate shear forces and maintain tissue integrity. While the C terminal of desmoplakin, composed of three plakin repeat domains and a linker domain, is in charge of intermediate filament binding, the N terminal end, consisting of a plakin domain (PD), is responsible for plaque attachment and interaction with other desmosomal components. Such critical interactions have been First of all, I would like to thank my supervisor Prof. Richard E. Palmer for giving me the opportunity to undertake a PhD at the University of Birmingham as a member of the NPRL group, and for all his ideas, guidance and support. I would also like to thank my co-supervisors Dr. Martyn Chidgey and Prof. Michael Overduin for opening the doors to the Laboratory of Structural Biology and NMR at the School of Cancer Sciences, and for their teaching and patience. I am also grateful to CONACyT for funding my PhD.
BioNanoScience, 2014
ABSTRACT We exploit the immobilization of proteins by size-selected atomic gold clusters to exami... more ABSTRACT We exploit the immobilization of proteins by size-selected atomic gold clusters to examine the plakin domain of desmoplakin (PD), a human desmosomal protein that is mutated in severe skin diseases and cardiomyopathy, using atomic force microscopy (AFM) in the liquid phase. Contact mode AFM indicates that the PD does not establish a covalent bond size-selected gold nanocluster supported on a graphite substrate, but tapping mode AFM images indicate enhanced weak adsorption. The protein dimensions obtained are compared with predicted values based on electron microscopy, small-angle X-ray scattering (SAXS) and X-ray crystallographic studies.
In this work we present the results of the application of the "light attenuation" metho... more In this work we present the results of the application of the "light attenuation" method to extract position information out of a large bi- dimensional scintillating plate, to be used as a neutron detector.
The Journal of Physical Chemistry A, 2014
The immobilization of individual biological molecules by metal nanoparticles requires that the pa... more The immobilization of individual biological molecules by metal nanoparticles requires that the particles themselves be immobilized. We introduce a new technique for immobilization of gold clusters based on their binding to small tunnels in a graphite support, themselves created by the implantation of small clusters. These tunnels are shown to perform as more effective cluster immobilization sites than point defects on the surface of graphite. The method is tested with atomic force microscopy (AFM) (both contact and noncontact mode) scanning. Size-selected clusters with 923, 561, 309, and 147 atoms have been immobilized and imaged with high-resolution, noncontact AFM.
The European Physical Journal A, 2009
Angular distributions were measured for neutron elastically scattered by nat Pb at 2.9, 3.0, 3.1,... more Angular distributions were measured for neutron elastically scattered by nat Pb at 2.9, 3.0, 3.1, 3.2 and 3.4 MeV at very forward angles. The mono-energetic neutron flux was produced at the tandem accelerator facility of the National Institute of Nuclear Research (ININ), Mexico, using the Associated Particle Technique (APT) in the D(d, n) 3 He reaction. Optical model predictions with best potential systematic show a fairly good agreement with our data, and also the need for a better understanding of the neutron scattering process at very small angles from the theoretical point of view.
Revista mexicana de …, 2007
... INIST Diffusion. 2, Allée du Parc de Brabois F-54514 Vandoeuvre-lès-Nancy Cedex France Phone:... more ... INIST Diffusion. 2, Allée du Parc de Brabois F-54514 Vandoeuvre-lès-Nancy Cedex France Phone: +33 (0)3 83 50 46 64 Fax: +33 (0)3 83 50 46 66. ...
with specic help available everywhere you see the i O symbol. The following versions of software ... more with specic help available everywhere you see the i O symbol. The following versions of software and data (see references i O) were used in the production of this report:
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Papers by Penelope Rodriguez-Zamora